--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trim.py	Mon Aug 29 05:44:57 2016 -0400
@@ -0,0 +1,59 @@
+import argparse
+
+#docs.python.org/dev/library/argparse.html
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", help="Input fasta")
+parser.add_argument("--output", help="Output fasta")
+parser.add_argument("--start", help="How many nucleotides to trim from the start", type=int)
+parser.add_argument("--end", help="How many nucleotides to trim from the end", type=int)
+
+args = parser.parse_args()
+start = int(args.start)
+end = int(args.end)
+
+print args.input
+print args.output
+print start
+print end
+
+if end <= 0 and start <= 0:
+	import shutil
+	shutil.copy(args.input, args.output)
+	import sys
+	sys.exit()
+	
+
+
+currentSeq = ""
+currentId = ""
+
+if end is 0:
+	with open(args.input, 'r') as i:
+		with open(args.output, 'w') as o:
+			for line in i.readlines():
+				if line[0] is ">":
+					currentSeq = currentSeq[start:]
+					if currentSeq is not "" and currentId is not "":
+						o.write(currentId)
+						o.write(currentSeq + "\n")
+					currentId = line
+					currentSeq = ""
+				else:
+					currentSeq += line.rstrip()
+			o.write(currentId)
+			o.write(currentSeq[start:] + "\n")
+else:
+	with open(args.input, 'r') as i:
+		with open(args.output, 'w') as o:
+			for line in i.readlines():
+				if line[0] is ">":
+					currentSeq = currentSeq[start:-end]
+					if currentSeq is not "" and currentId is not "":
+						o.write(currentId)
+						o.write(currentSeq + "\n")
+					currentId = line
+					currentSeq = ""
+				else:
+					currentSeq += line.rstrip()
+			o.write(currentId)
+			o.write(currentSeq[start:-end] + "\n")